YDEB - BACSU - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

YDEB - Putative transcription factor YdeB

UniProt:	P96659	Sequences: MFQIGDNIVYPMHGAGIIEAIEEKEFLEEKQQYYVIRMSISNMTVMIPTSKILSSNIRPVTDILALKHIMHIFQHGESDRLLPWKQRYKINTDKIKTGEIQEGAEVVRDLMRMKKEKALNASEKKMLDNAYEFLISELEVIKGITEKQIKSFG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	153 (148)
Sequences:	1062 (730)
Seq/√Len:	60.0

BACSU - YDEB

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_Q	50_S	4.941	1.00
144_I	149_I	3.910	1.00
23_E	30_K	3.900	1.00
145_T	148_Q	3.842	1.00
66_L	138_L	3.593	1.00
19_E	37_R	3.496	1.00
22_E	35_V	3.487	1.00
8_I	57_I	3.341	1.00
23_E	32_Q	2.838	1.00
62_D	65_A	2.754	1.00
25_E	30_K	2.712	1.00
15_A	136_S	2.375	1.00
99_E	102_E	2.288	1.00
66_L	141_I	2.224	1.00
34_Y	49_T	2.078	1.00
7_N	17_I	2.074	1.00
84_W	123_E	1.913	1.00
35_V	46_M	1.895	1.00
24_K	46_M	1.847	1.00
16_G	36_I	1.843	1.00
84_W	120_N	1.827	1.00
70_M	74_Q	1.777	0.99
144_I	148_Q	1.743	0.99
32_Q	49_T	1.734	0.99
60_V	141_I	1.652	0.99
94_K	105_E	1.617	0.99
72_I	101_Q	1.553	0.98
4_I	20_A	1.553	0.98
13_H	110_L	1.533	0.98
9_V	15_A	1.515	0.98
94_K	106_V	1.493	0.98
64_L	68_H	1.443	0.98
120_N	123_E	1.317	0.96
61_T	100_I	1.298	0.95
67_K	71_H	1.262	0.95
60_V	140_V	1.215	0.93
97_T	102_E	1.207	0.93
138_L	149_I	1.193	0.93
86_Q	122_S	1.186	0.93
7_N	140_V	1.183	0.93
49_T	52_I	1.179	0.92
61_T	66_L	1.151	0.91
58_R	100_I	1.146	0.91
91_N	126_M	1.140	0.91
107_V	130_A	1.138	0.91
72_I	95_I	1.126	0.91
70_M	149_I	1.125	0.91
80_R	109_D	1.107	0.90
111_M	127_L	1.096	0.89
105_E	109_D	1.086	0.89
108_R	122_S	1.080	0.89
34_Y	57_I	1.080	0.89
58_R	137_E	1.077	0.88
104_A	138_L	1.074	0.88
65_A	99_E	1.073	0.88
51_K	55_S	1.049	0.87
51_K	54_S	1.049	0.87
86_Q	120_N	1.047	0.87
88_Y	123_E	1.045	0.87
80_R	83_P	1.043	0.87
2_F	59_P	1.039	0.87
15_A	118_A	1.031	0.86
85_K	122_S	1.030	0.86
47_I	55_S	1.023	0.86
18_I	70_M	1.004	0.85
33_Y	46_M	1.003	0.85
26_F	56_N	1.001	0.85
83_P	95_I	0.997	0.84
90_I	93_D	0.988	0.84
104_A	107_V	0.987	0.84
102_E	105_E	0.986	0.84
15_A	140_V	0.976	0.83
63_I	141_I	0.966	0.82
8_I	134_L	0.947	0.81
87_R	98_G	0.947	0.81
61_T	101_Q	0.936	0.80
63_I	67_K	0.929	0.80
73_F	104_A	0.927	0.80
5_G	28_E	0.926	0.80
88_Y	92_T	0.917	0.79
53_L	72_I	0.907	0.78
143_G	149_I	0.906	0.78
127_L	131_Y	0.904	0.78
76_G	95_I	0.892	0.77
19_E	68_H	0.881	0.76
5_G	17_I	0.878	0.76
88_Y	125_K	0.876	0.76
15_A	60_V	0.876	0.76
61_T	65_A	0.871	0.75
104_A	134_L	0.870	0.75
37_R	42_N	0.861	0.74
83_P	86_Q	0.845	0.73
3_Q	32_Q	0.845	0.73
107_V	134_L	0.838	0.72
131_Y	135_I	0.837	0.72
83_P	97_T	0.833	0.72
100_I	134_L	0.832	0.72
11_P	56_N	0.827	0.71
11_P	98_G	0.824	0.71
65_A	141_I	0.824	0.71
80_R	87_R	0.820	0.71
93_D	116_E	0.814	0.70
18_I	34_Y	0.809	0.70
132_E	146_E	0.802	0.69
3_Q	21_I	0.798	0.69
63_I	142_K	0.792	0.68
32_Q	71_H	0.789	0.68
94_K	97_T	0.774	0.66
145_T	149_I	0.772	0.66
111_M	135_I	0.759	0.65
84_W	87_R	0.758	0.65
13_H	120_N	0.751	0.64
110_L	133_F	0.751	0.64
2_F	83_P	0.749	0.64
76_G	108_R	0.746	0.63
68_H	101_Q	0.742	0.63
63_I	68_H	0.741	0.63
59_P	149_I	0.739	0.63
10_Y	110_L	0.732	0.62
88_Y	126_M	0.725	0.61
106_V	124_K	0.724	0.61
66_L	142_K	0.722	0.61
75_H	108_R	0.717	0.60
11_P	100_I	0.711	0.60
6_D	147_K	0.710	0.60
113_M	118_A	0.708	0.59
6_D	139_E	0.706	0.59
45_V	97_T	0.705	0.59
123_E	126_M	0.703	0.59
36_I	131_Y	0.703	0.59
15_A	133_F	0.703	0.59
56_N	124_K	0.700	0.59
65_A	70_M	0.697	0.58
22_E	46_M	0.696	0.58
88_Y	91_N	0.690	0.57
64_L	67_K	0.690	0.57
11_P	16_G	0.686	0.57
72_I	108_R	0.683	0.57
36_I	52_I	0.682	0.57
53_L	147_K	0.676	0.56
29_E	59_P	0.675	0.56
115_K	149_I	0.674	0.56
43_M	98_G	0.671	0.55
3_Q	65_A	0.671	0.55
29_E	145_T	0.667	0.55
85_K	88_Y	0.664	0.55
16_G	38_M	0.662	0.54
84_W	124_K	0.658	0.54
57_I	121_A	0.657	0.54
18_I	21_I	0.652	0.53
66_L	149_I	0.649	0.53
81_L	95_I	0.639	0.52
59_P	143_G	0.639	0.52
103_G	134_L	0.637	0.52
60_V	89_K	0.634	0.51
87_R	106_V	0.632	0.51
63_I	145_T	0.629	0.51
68_H	143_G	0.628	0.51
34_Y	52_I	0.626	0.50
85_K	120_N	0.623	0.50
84_W	106_V	0.621	0.50
37_R	44_T	0.619	0.50
49_T	142_K	0.618	0.49
10_Y	45_V	0.617	0.49
36_I	47_I	0.613	0.49
106_V	133_F	0.613	0.49
33_Y	121_A	0.609	0.48
26_F	124_K	0.608	0.48
13_H	43_M	0.604	0.48
11_P	47_I	0.598	0.47
15_A	121_A	0.596	0.47
87_R	110_L	0.590	0.46
113_M	133_F	0.589	0.46
79_D	112_R	0.587	0.46
106_V	126_M	0.582	0.45
18_I	36_I	0.580	0.45
92_T	95_I	0.575	0.45
142_K	149_I	0.572	0.44
3_Q	49_T	0.570	0.44
114_K	131_Y	0.567	0.44
83_P	99_E	0.565	0.43
40_I	132_E	0.564	0.43
5_G	126_M	0.563	0.43
88_Y	106_V	0.563	0.43
64_L	69_I	0.562	0.43
44_T	82_L	0.560	0.43
31_Q	34_Y	0.557	0.43
23_E	147_K	0.556	0.43
10_Y	55_S	0.553	0.42
50_S	59_P	0.552	0.42
7_N	54_S	0.548	0.42
60_V	103_G	0.548	0.42
42_N	148_Q	0.548	0.42
83_P	88_Y	0.545	0.41
118_A	126_M	0.545	0.41
18_I	133_F	0.545	0.41
107_V	123_E	0.539	0.41
20_A	49_T	0.536	0.40
43_M	46_M	0.536	0.40
18_I	62_D	0.534	0.40
3_Q	68_H	0.531	0.40
69_I	103_G	0.528	0.39
15_A	40_I	0.526	0.39
74_Q	148_Q	0.525	0.39
91_N	134_L	0.525	0.39
45_V	131_Y	0.523	0.39
52_I	70_M	0.522	0.39
71_H	147_K	0.521	0.39
11_P	110_L	0.520	0.39
93_D	117_K	0.518	0.38
32_Q	143_G	0.518	0.38
12_M	15_A	0.516	0.38
18_I	37_R	0.516	0.38
45_V	99_E	0.515	0.38
68_H	71_H	0.512	0.38
55_S	125_K	0.511	0.38
36_I	73_F	0.509	0.37
69_I	72_I	0.506	0.37
32_Q	50_S	0.502	0.37
42_N	121_A	0.500	0.37
111_M	126_M	0.500	0.37
87_R	120_N	0.500	0.37

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
2lwjA	1	1	100	0.227	Contact Map
4kbmB	1	0.9281	100	0.234	Contact Map
4l5gA	1	1	100	0.263	Contact Map
2lt3A	1	0.6863	99.9	0.485	Contact Map
2lt4A	1	0.4248	99.8	0.606	Contact Map
2lt1A	1	0.4183	99.7	0.611	Contact Map
3mlqE	1	0.3072	99.6	0.647	Contact Map
2eyqA	1	0.8627	97.7	0.828	Contact Map
4c2tA	1	0	56.5	0.92	Contact Map
1pjrA	1	0	52.3	0.922	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

Page generated in 0.0064 seconds.